Sökning: onr:"swepub:oai:lup.lub.lu.se:ff94e0df-eb42-4aa5-a54d-a958094e2bb6" > Genomic basis for R...
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000 | 08981naa a2201117 4500 | |
001 | oai:lup.lub.lu.se:ff94e0df-eb42-4aa5-a54d-a958094e2bb6 | |
003 | SwePub | |
008 | 230329s2020 | |||||||||||000 ||eng| | |
009 | oai:prod.swepub.kib.ki.se:143704363 | |
024 | 7 | a https://lup.lub.lu.se/record/ff94e0df-eb42-4aa5-a54d-a958094e2bb62 URI |
024 | 7 | a https://doi.org/10.1038/s41586-020-1970-02 DOI |
024 | 7 | a http://kipublications.ki.se/Default.aspx?queryparsed=id:1437043632 URI |
040 | a (SwePub)lud (SwePub)ki | |
041 | a engb eng | |
042 | 9 SwePub | |
072 | 7 | a art2 swepub-publicationtype |
072 | 7 | a ref2 swepub-contenttype |
100 | 1 | a Calabrese, Claudiau European Bioinformatics Institute4 aut |
245 | 1 0 | a Genomic basis for RNA alterations in cancer |
264 | c 2020-02-05 | |
264 | 1 | b Springer Science and Business Media LLC,c 2020 |
520 | a Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer. | |
650 | 7 | a MEDICIN OCH HÄLSOVETENSKAPx Medicinska och farmaceutiska grundvetenskaperx Medicinsk genetik0 (SwePub)301072 hsv//swe |
650 | 7 | a MEDICAL AND HEALTH SCIENCESx Basic Medicinex Medical Genetics0 (SwePub)301072 hsv//eng |
650 | 7 | a NATURVETENSKAPx Biologix Bioinformatik och systembiologi0 (SwePub)106102 hsv//swe |
650 | 7 | a NATURAL SCIENCESx Biological Sciencesx Bioinformatics and Systems Biology0 (SwePub)106102 hsv//eng |
653 | a DNA Copy Number Variations | |
653 | a DNA, Neoplasm | |
653 | a Gene Expression Regulation, Neoplastic | |
653 | a Genome, Human | |
653 | a Genomics | |
653 | a Humans | |
653 | a Neoplasms/genetics | |
653 | a RNA/genetics | |
653 | a Transcriptome | |
700 | 1 | a Davidson, Natalie Ru ETH Zürich4 aut |
700 | 1 | a Demircioğlu, Denizu National University of Singapore4 aut |
700 | 1 | a Fonseca, Nuno Au European Bioinformatics Institute4 aut |
700 | 1 | a He, Yaou Peking University4 aut |
700 | 1 | a Kahles, Andréu ETH Zürich4 aut |
700 | 1 | a Lehmann, Kjong-Vanu ETH Zürich4 aut |
700 | 1 | a Liu, Fenglinu Peking University4 aut |
700 | 1 | a Shiraishi, Yuichiu University of Tokyo4 aut |
700 | 1 | a Soulette, Cameron Mu University of California, Santa Cruz4 aut |
700 | 1 | a Urban, Larau European Bioinformatics Institute4 aut |
700 | 1 | a Greger, Lilianau European Bioinformatics Institute4 aut |
700 | 1 | a Li, Siliangu Beijing Genomics Institute4 aut |
700 | 1 | a Liu, Dongbingu Beijing Genomics Institute4 aut |
700 | 1 | a Perry, Marc Du Ontario Institute for Cancer Research4 aut |
700 | 1 | a Xiang, Qianu Ontario Institute for Cancer Research4 aut |
700 | 1 | a Zhang, Fanu Peking University4 aut |
700 | 1 | a Zhang, Junjunu Ontario Institute for Cancer Research4 aut |
700 | 1 | a Bailey, Peteru University of Glasgow4 aut |
700 | 1 | a Erkek, Serapu European Molecular Biology Laboratory Heidelberg4 aut |
700 | 1 | a Hoadley, Katherine Au University of North Carolina4 aut |
700 | 1 | a Hou, Yongu Beijing Genomics Institute4 aut |
700 | 1 | a Huska, Matthew Ru Berlin Institute for Medical Systems Biology4 aut |
700 | 1 | a Kilpinen, Helenau University College London4 aut |
700 | 1 | a Korbel, Jan Ou European Molecular Biology Laboratory Heidelberg4 aut |
700 | 1 | a Marin, Maximillian Gu University of California, Santa Cruz4 aut |
700 | 1 | a Markowski, Juliau Berlin Institute for Medical Systems Biology4 aut |
700 | 1 | a Nandi, Tannisthau A*Star, Genome Institute of Singapore (GIS)4 aut |
700 | 1 | a Pan-Hammarström, Qiangu Karolinska Institutet4 aut |
700 | 1 | a Pedamallu, Chandra Sekharu Broad Institute4 aut |
700 | 1 | a Siebert, Reineru University Hospital of Ulm,University of Ulm4 aut |
700 | 1 | a Stark, Stefan Gu ETH Zürich4 aut |
700 | 1 | a Su, Hongu Beijing Genomics Institute4 aut |
700 | 1 | a Tan, Patricku A*Star, Genome Institute of Singapore (GIS)4 aut |
700 | 1 | a Waszak, Sebastian Mu European Molecular Biology Laboratory Heidelberg4 aut |
700 | 1 | a Yung, Christinau Ontario Institute for Cancer Research4 aut |
700 | 1 | a Zhu, Shidau Beijing Genomics Institute4 aut |
700 | 1 | a Awadalla, Philipu Ontario Institute for Cancer Research4 aut |
700 | 1 | a Creighton, Chad Ju Baylor College of Medicine4 aut |
700 | 1 | a Meyerson, Matthewu Broad Institute4 aut |
700 | 1 | a Ouellette, B F Francisu University of Toronto4 aut |
700 | 1 | a Wu, Kuiu Beijing Genomics Institute4 aut |
700 | 1 | a Yang, Huanmingu Beijing Genomics Institute4 aut |
700 | 1 | a Brazma, Alvisu European Bioinformatics Institute4 aut |
700 | 1 | a Brooks, Angela Nu University of California, Santa Cruz4 aut |
700 | 1 | a Göke, Jonathanu A*Star, Genome Institute of Singapore (GIS)4 aut |
700 | 1 | a Rätsch, Gunnaru ETH Zürich4 aut |
700 | 1 | a Schwarz, Roland Fu European Bioinformatics Institute4 aut |
700 | 1 | a Stegle, Oliveru European Bioinformatics Institute4 aut |
700 | 1 | a Zhang, Zeminu Peking University4 aut |
700 | 1 | a Borg, Åkeu Lund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Familjär bröstcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine,Familial Breast Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments4 cre0 (Swepub:lu)onk-abo |
700 | 1 | a Ringnér, Markusu Lund University,Lunds universitet,Molekylär cellbiologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Molecular Cell Biology,Department of Biology,Faculty of Science4 cre0 (Swepub:lu)thep-mri |
700 | 1 | a Staaf, Johanu Lund University,Lunds universitet,Avdelningen för translationell cancerforskning,Institutionen för laboratoriemedicin,Medicinska fakulteten,Forskningsgrupp Lungcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Bröst/lungcancer,Sektion I,Institutionen för kliniska vetenskaper, Lund,Division of Translational Cancer Research,Department of Laboratory Medicine,Faculty of Medicine,Research Group Lung Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments,Breast/lungcancer,Section I,Department of Clinical Sciences, Lund4 cre0 (Swepub:lu)onk-jst |
710 | 2 | a European Bioinformatics Instituteb ETH Zürich4 org |
710 | 2 | a PCAWG Transcriptome Core Group |
710 | 2 | a PCAWG Consortium |
773 | 0 | t Natured : Springer Science and Business Media LLCg 578:7793, s. 129-136q 578:7793<129-136x 0028-0836x 1476-4687 |
856 | 4 | u http://dx.doi.org/10.1038/s41586-020-1970-0x freey FULLTEXT |
856 | 4 | u https://www.nature.com/articles/s41586-020-1970-0.pdf |
856 | 4 8 | u https://lup.lub.lu.se/record/ff94e0df-eb42-4aa5-a54d-a958094e2bb6 |
856 | 4 8 | u https://doi.org/10.1038/s41586-020-1970-0 |
856 | 4 8 | u http://kipublications.ki.se/Default.aspx?queryparsed=id:143704363 |
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